To close this thread, on centos7 'git annex' is an invalid command. That can be fixed with


yum install epel-release
yum install git-annex

git-annex get --metadata fstags=makeinstall .


Now the 'make install' finishes without errors.


-Henk

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Meij, Henk <hmeij@wesleyan.edu>
Sent: Saturday, November 18, 2017 11:28:09 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] cuda compile help
 

And that ofcourse was the partial answer, as listed on wiki page, I need to apply a data dir,, these links are pointing to missing files. Will retry Monday.


-Henk


[hmeij@n78 freesurfer-gpu.git]$ find . -name *glnxa64* -exec ls -l {} \;
lrwxrwxrwx 1 hmeij its 195 Nov 17 08:14 ./scripts/fs_spmreg.glnxa64 -> ../.git/annex/objects/9g/2q/SHA256E-s13078893--f1e2a2ea60c0ad9ed4119bae45feed10cb866b93bf484340ada79a496ca5754a/SHA256E-s13078893--f1e2a2ea60c0ad9ed4119bae45feed10cb866b93bf484340ada79a496ca5754a
lrwxrwxrwx 1 hmeij its 196 Nov 17 08:14 ./fsfast/bin/fast_selxavg3b.glnxa64 -> ../../.git/annex/objects/5P/qx/SHA256E-s6879505--d26c8f55485cd9baea74afc6e34ae48e0384452ff76d498a08b648a4ecb26bce/SHA256E-s6879505--d26c8f55485cd9baea74afc6e34ae48e0384452ff76d498a08b648a4ecb26bce
lrwxrwxrwx 1 hmeij its 194 Nov 17 08:14 ./fsfast/bin/mkcontrast2m.glnxa64 -> ../../.git/annex/objects/P7/77/SHA256E-s105002--bd8037b6bf7bbb40ea5ca7b831b79cbbe5762d8c98f68b41efaf1a6065ec87f4/SHA256E-s105002--bd8037b6bf7bbb40ea5ca7b831b79cbbe5762d8c98f68b41efaf1a6065ec87f4


From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Meij, Henk <hmeij@wesleyan.edu>
Sent: Friday, November 17, 2017 6:35:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cuda compile help
 
I should have mentioned, i did not do any data dirs step, confused on this, just hoping to compile gpu code 

-Henk



----- Reply message -----
From: "Meij, Henk" <hmeij@wesleyan.edu>
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] cuda compile help
Date: Fri, Nov 17, 2017 6:24 PM

cuda v8 freesurfer git download from today (v6?), gtx1080ti gpus, brief env recap:


  999  cd /usr/local/freesurfer-gpu.git/
 1001  export PATH=/usr/local/cuda-8.0/bin:$PATH
 1002  export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64
 1004  make clean
 1008  ./setup_configure | tee -a setup_configure.log
 1011  ./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda-8.0 | tee -a configure.log
 1012  time make -j4 | tee -a make.log
 1013  make install


[hmeij@n78 freesurfer-gpu.git]$ grep nvcc Makefile
NVCC = /usr/local/cuda-8.0/bin/nvcc



Q1 what causes this and how to fix, make install fails
/bin/install -c fs_spmreg.glnxa64 irepifitvol.glnx64 /usr/local/freesurfer-6.0.0/bin
/bin/install: cannot stat â_spmreg.glnxa64âNo such file or directory
/bin/install: cannot stat âepifitvol.glnx64âNo such file or directory
make[2]: *** [install-data-local] Error 1
make[2]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts'
make: *** [install-recursive] Error 1


Q2 no cuda packages, maybe related to Q1

[hmeij@n78 freesurfer-gpu.git]$ ls /usr/local/freesurfer-6.0.0/bin/*cuda*
/usr/local/freesurfer-6.0.0/bin/cuda_setup



Thanks for any help.
-Henk